archive-nlmnlp

name	archive-nlmnlp
description	Use when maintaining a local NLM NLP concept archive over PubMed for offline chemical, disease, gene, or GeneRIF lookups.
disable-model-invocation	true
user-invocable	true

archive-nlmnlp

Quick Start

• Command: archive-nlmnlp [daily|-index]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/archive-nlmnlp
• Full reference: See references/help.md for complete documentation

When To Use This Tool

• Build a local PubMed concept archive backed by PubTator Central, GeneRIF, and gene metadata files.
• Support offline lookup of chemical, disease, gene, synonym, and GeneRIF-derived postings in EDirect workflows.
• Refresh the archive after upstream concept files change, then rebuild postings in the usual EDirect layout.
• Use this instead of stitching together the PubTator and GeneRIF files manually.

Common Patterns

# 1) Refresh the local NLM NLP extras and archive over HTTPS
export EDIRECT_LOCAL_ARCHIVE=/data/edirect
archive-nlmnlp -https

# 2) Rebuild only the incremental index and invert layers
archive-nlmnlp daily

# 3) Rebuild merged postings for downstream local searching
archive-nlmnlp -index

Recommended Workflow

1. Set EDIRECT_LOCAL_ARCHIVE and confirm the archive root exists and is writable.
2. Make sure pm-setup, pm-prepare, and the local Go toolchain are available.
3. Run archive-nlmnlp or archive-nlmnlp -https to stage the latest PubTator / GeneRIF support files.
4. Follow with daily or -index as a separate command when you need refreshed postings.
5. Check the DWN, IDX, INV, MRG, and PST timing blocks to confirm each stage actually ran.

Guardrails

• --help and --version are not safe inspection switches; they still trigger archive setup and prerequisite checks.
• The script depends on EDIRECT_LOCAL_ARCHIVE, pm-setup, pm-prepare, and a local go compiler.
• Default transport may try the FTP / Aspera path; use -https or -ftp explicitly if you need predictable transfer behavior.
• Cleaning and indexing must be run separately.
• The cleanup aliases remove scratch data, so do not use them casually on a populated archive.